PUBLICATION

Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm

Authors
Wu, S.F., Zhang, H., and Cairns, B.R.
ID
ZDB-PUB-110317-42
Date
2011
Source
Genome research   21(4): 578-89 (Journal)
Registered Authors
Wu, Shan-Fu
Keywords
none
Datasets
GEO:GSE26609
MeSH Terms
  • Animals
  • Chromatin/genetics*
  • Chromatin/metabolism*
  • DNA Methylation/genetics
  • Embryonic Development/genetics*
  • Gene Expression Regulation, Developmental
  • Genome/genetics
  • Histones/metabolism
  • Male
  • RNA, Untranslated/genetics
  • RNA, Untranslated/metabolism
  • Repetitive Sequences, Nucleic Acid/genetics
  • Spermatozoa/cytology
  • Spermatozoa/metabolism*
  • Time Factors
  • Zebrafish/embryology*
  • Zebrafish/genetics*
PubMed
21383318 Full text @ Genome Res.
Abstract
In mature human sperm, genes of importance for embryo development (i.e., transcription factors) lack DNA methylation and bear nucleosomes with distinctive histone modifications, suggesting the specialized packaging of these developmental genes in the germline. Here, we explored the tractable zebrafish model and found conceptual conservation as well as several new features. Biochemical and mass spectrometric approaches reveal the zebrafish sperm genome packaged in nucleosomes and histone variants (and not protamine), and we find linker histones high and H4K16ac absent, key factors that may contribute to genome condensation. We examined several activating (H3K4me2/3, H3K14ac, H2AFV) and repressing (H3K27me3, H3K36me3, H3K9me3, hypoacetylation) modifications/compositions genome-wide and find developmental genes packaged in large blocks of chromatin with coincident activating and repressing marks and DNA hypomethylation, revealing complex "multivalent" chromatin. Notably, genes that acquire DNA methylation in the soma (muscle) are enriched in transcription factors for alternative cell fates. Remarkably, whereas H3K36me is located in the 3' coding region of heavily transcribed genes in somatic cells, H3K36me is present in the promoters of "silent" developmental regulators in sperm, suggesting different rules for H3K36me3 in the germline and soma. We also reveal the chromatin patterns of transposons, rDNA, and tDNAs. Finally, high levels of H3K4me3 and H3K14ac in sperm are correlated with genes activated in embryos prior to the mid-blastula transition (MBT), whereas multivalent genes are correlated with activation at or after MBT. Taken together, gene sets with particular functions in the embryo are packaged by distinctive types of complex and often atypical chromatin in sperm.
Genes / Markers
Figures
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping